Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

Structural investigation of resorcinol based symmetrical banana mesogens by XRD, NMR and polarization measurements

Synthesis and structural characterization of two novel symmetrical banana mesogens built from resorcinol with seven phenyl rings linked by ester and imine with a terminal dodecyl/dodecyloxy chain has been carried out. Density functional theory (DFT) has been employed for obtaining the geometry optimized structures, the dipole moments and C-13 NMR chemical shifts. The HOPM and DSC studies revealed enantiotropic B-2 and B-7 phases for the dodecyl and dodecyloxy homologs respectively. The powder X-ray studies of both the mesogens indicate the presence of layer ordering. The polarization measurements reveal an anti-ferroelectric switching for the B-2 phase of the dodecyl homolog whose structure has been identified as SmCSPA. The B-7 phase of the dodecyloxy homolog was found to be non-switchable. High resolution C-13 NMR study of the dodecyl homolog in its mesophase has been carried out. C-13-H-1 dipolar couplings obtained from the 2-dimensional separated local field spectroscopy experiment were used to obtain the orientational order parameters of the different segments of the mesogen. Very large C-13-H-1 dipolar couplings observed for the carbons of the central phenyl ring (9.7-12.3 kHz) in comparison to the dipolar couplings of those of the side arm phenyl rings (less than 3 kHz) are a direct consequence of the ordering in the banana phase and the shape of the molecule. From the ratio of the local order parameter values, the bent-angle of the mesogen could be determined in a straight forward manner to be 120.5 degrees.

New single-source precursor for bismuth sulfide and its use as low-cost counter electrode material for dye-sensitized solar cells

One new homoleptic Bi(dtc)(3)] (1) (dtc = 4-hydroxypiperdine dithiocarbamate) has been synthesized and characterized by microanalysis, IR, UV-Vis, H-1 and C-13 spectroscopy and X-ray crystallography. The photoluminescence spectrum for the compound in DMSO solution was recorded. The crystal structure of 1 displayed distorted octahedral geometry around the Bi(III) center bonded through sulfur atoms of the dithiocarbamate ligands. TGA indicates that the compound decomposes to a Bi and Bi-S phase system. The Bi and Bi-S obtained from decomposition of the compound have been characterized by pXRD, EDAX and SEM. Solvothermal decomposition of 1 in the absence and presence of two different capping agents yielded three morphologically different Bi2S3 systems which were deployed as counter-electrode in dye-sensitized solar cells (DSSCs). (C) 2015 Elsevier B.V. All rights reserved.

Effect of Manganese (II) Oxide on microstructure and ionic transport properties of nanostructured cubic zirconia

Effect of MnO addition on microstructure and ionic transport properties of nanocrystalline cubic(c)-ZrO2 is reported. Monoclinic (m) ZrO2 powders with 10-30 mol% MnO powder are mechanically alloyed in a planetary ball mill at room temperature for 10 h and annealed at 550 degrees C for 6 h. In all compositions m-ZrO2 transforms completely to nanocrystalline c-ZrO2 phase and MnO is fully incorporated into c-ZrO2 lattice. Rietveld's refinement technique is employed for detailed microstructure analysis by analyzing XRD patterns. High resolution transmission electron microscopy (HRTEM) analysis confirms the complete formation of c-ZrO2 phase. Presence of stoichiometric Mn in c-ZrO2 powder is confirmed by Electron Probe Microscopy analysis. XPS analysis reveals that Mn is mostly in Mn2+ oxidation state. A correlation between lattice parameter and oxygen vacancy is established. A detailed ionic conductivity measurement in the 250 degrees-575 degrees C temperature range describes the effect of MnO on conductivity of c-ZrO2. The ionic conductivity (s) of 30 mol% MnO alloyed ZrO2 at 550 degrees C is 0.04 s cm(-1). Electrical relaxation studies are carried out by impedance and modulus spectroscopy. Relaxation frequency is found to increase with temperature and MnO mol fraction. Electrical characterization predicts that these compounds have potentials for use as solid oxide fuel cell electrolyte material. (C) 2015 Elsevier Ltd. All rights reserved.

Stable isotope evidence for ca. 2.7-Ga-old Archean cap carbonates from the Dharwar Supergroup, southern India

Carbon isotope compositions of carbonate rocks from similar to 2.7-Ga-old Neoarchean Vanivilas Formation of the Dharwar Supergroup presented earlier by us are re-evaluated in this study, besides oxygen isotope compositions of a few silica dolomite pairs. The purpose of such a revisit assumes significance in view of recent field evidences that suggest a glaciomarine origin for the matrix-supported conglomerate member, the Talya conglomerate, which underlies the carbonate rocks of the Vanivilas Formation. An in-depth analysis of carbon isotope data reveals preservation of their pristine character despite the rocks having been subjected to metamorphism to different degrees (from lower greenschist to lower amphibolite facies). The dolomitic member of Vanivilas Formation of Marikanive area is characterized by highly depleted delta C-13 value (up to -5 parts per thousand VPDB) and merits as the Indian example of ca. 2.7-Ga-old cap carbonate. This inference is further supported by estimated low temperature of equilibration documented by a few silica dolomite pairs from the Vanivilas Formation collected near Kalche area. These pairs show evidence for oxygen isotopic equilibrium at low temperatures (similar to 0-20 degrees C) with depleted water (delta O-18 = -21 parts per thousand to -15 parts per thousand VSMOW) of glacial origin. We propose that the mineral pairs were deposited during the deglaciation period when the ocean temperature was in its gradual restoration phase. The dolomite of Marikanive area is the first record of cap carbonates from the Indian subcontinent with Neoarchean antiquity.

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid-crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, H-1-C-13 dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two-dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.

The influence of termites on soil sheeting properties varies depending on the materials on which they feed

Fungus-growing termites are involved in many ecological processes and play a central role in influencing soil dynamics in the tropics. The physical and chemical properties of their nest structures have been largely described; however less information is available concerning the relatively temporary structures made above-ground to access food items and protect the foraging space (the soil `sheetings'). This study investigated whether the soil physical and chemical properties of these constructions are constant or if they vary depending on the type of food they cover. Soil samples and soil sheetings were collected in a forest in India, from leaves on the ground (LEAF), fallen branches (WOOD), and vertical soil sheetings covering the bark of trees (TREE). In this environment, termite diversity was dominated by Odontotermes species, and especially Odontotermes feae and Odontotermes obesus. However, there was no clear niche differentiation and, for example, O. feae termites were found on all the materials. Compared with the putative parent soil (control), TREE sheetings showed the greatest (and most significant) differences (higher clay content and smaller clay particle sizes, lower C and N content and smaller delta C-13 and delta N-15), while LEAF sheetings were the least modified, though still significantly different than the control soil. We suggest that the termite diversity is a less important driver of potential soil modification than sheeting diversity. Further, there is evidence that construction properties are adapted to their prospective life-span, with relatively long-lasting structures being most different from the parent soil. (C) 2015 Elsevier Masson SAS. All rights reserved.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Stable isotopic signature of Southern Ocean deep water CO2 ventilation

The link between atmospheric CO2 level and ventilation state of the deep ocean is poorly understood due to the lack of coherent observations on the partitioning of carbon between atmosphere and ocean. In this Southern Ocean study, we have classified the Southern Ocean into different zones based on its hydrological features and have binned the variability in latitudinal air-CO2 concentration and its isotopic ratios. Together with air-CO2, we analysed the surface water for the isotopic ratios in dissolved inorganic carbon (DIC). Using the binary mixing approach on the isotopic ratio of atmospheric CO2 and its concentration, we identified the delta C-13 value of source CO2. The isotopic composition of source CO2 was around -9.22 +/- 0.26 parts per thousand for the year 2011 and 2012, while a composition of -13.49 +/- 4.07 parts per thousand was registered for the year 2013. We used the delta C-13 of DIC to predict the CO2 composition in air under equilibrium and compared our estimates with actual observations. We suggest that the degeneration of the DIC in presence of warm water in the region was the factor responsible for adding the CO2 to the atmosphere above. The place of observation coincides with the zone of high wind speed which promotes the process of CO2 exsolution from sea water. (C) 2015 Elsevier Ltd. All rights reserved.

New symmetrical dinucleating ligand based assembly of bridged dicopper(II) and dizinc(II) centers: Synthesis, structure, spectroscopy, magnetic properties and glycoside hydrolysis

Two dinuclear copper(II) complexes Li(H2O)(3)(CH3OH)](4)Cu2Br4]Cu-2(cpdp)(mu-O2CCH3)](4)(OH)(2) (1), Cu (H2O)(4)]Cu-2(cpdp)(mu-O2CC6H5)](2)Cl-2 center dot 5H(2)O (2), and a dinuclear zinc(II) complex Zn-2(cpdp)(mu-O2CCH3)] (3) have been synthesized using pyridine and benzoate functionality based new symmetrical dinucleating ligand, N, N'-Bis2-carboxybenzomethyl]-N, N'-Bis2-pyridylmethyl]-1,3-diaminopropan-2-ol (H(3)cpdp). Complexes 1, 2 and 3 have been synthesized by carrying out reaction of the ligand H3cpdp with stoichiometric amounts of Cu-2(O2CCH3)(4)(H2O)(2)], CuCl2 center dot 2H(2)O/C6H5COONa, and Zn(CH3COO)(2)center dot 2H(2)O, respectively, in methanol in the presence of NaOH at ambient temperature. Characterizations of the complexes have been done using various analytical techniques including single crystal X-ray structure determination. The X-ray crystal structure analyses reveal that the copper(II) ions in complexes 1 and 2 are in a distorted square pyramidal geometry with Cu-Cu separation of 3.455(8) angstrom and 3.492(1)angstrom, respectively. The DFT optimized structure of complex 3 indicates that two zinc(II) ions are in a distorted square pyramidal geometry with Zn-Zn separation of 3.492(8)angstrom. UV-Vis and mass spectrometric analyses of the complexes confirm their dimeric nature in solution. Furthermore, H-1 and C-13 NMR spectroscopic investigations authenticate the integrity of complex 3 in solution. Variable-temperature (2-300 K) magnetic susceptibility measurements show the presence of antiferromagnetic interactions between the copper centers, with J = -26.0 cm(-1) and -23.9 cm(-1) ((H) over cap = -2JS(1)S(2)) in complexes 1 and 2, respectively. In addition, glycosidase-like activity of the complexes has been investigated in aqueous solution at pH similar to 10.5 by UV-Vis spectrophotometric technique using p-nitrophenyl-alpha-D-glucopyranoside (4) and p-nitrophenyl-beta-D-glucopyranoside (5) as model substrates. (C) 2015 Elsevier B.V. All rights reserved.

Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum

Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) C-13-H-1] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a ``uniqueness score'' and a ``coverage score''. Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of deduttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMIR-based metabolomics data by reducing existing impediments.

A new synthesis of Entacapone and report on related studies

A new synthesis of the catechol-O-methyltransferase (COMT) inhibitor, entacapone (E-isomer) has been achieved under mild conditions by amine-mediated demethylation of the precursor 2-Cyano-3-(3- hydroxy-4-methoxy-5-nitrophenyl) prop-2-eneamide, wherein the methoxyl group adjacent to a nitro group gets demethylated under nucleophilic attack. Similar demethylation was achieved on ethyl 2-cyano-3-(3, 4-dimethoxy-5-nitrophenyl) prop-2-enoate, 2-cyano-3-(3,4-dimethoxy-5-nitrophenyl)-N,N-diethylprop-2-enamide, ethyl 2-cyano-3-(3-hydroxy-4-methoxy-5-nitrophenyl) prop-2-enoate and ethyl 2-cyano-3-(4-methoxy-3-nitrophenyl) prop-2-enoate. The scope of demethylation has been studied. Analogues of ethyl 2-cyano-3-(3, 4-dimethoxy-5-nitrophenyl) prop-2-enoate wherein a methoxyl group is not adjacent to a NO (2) group are unaffected and phenolic derivatives yield the amine salts. Entacapone has been converted to salts with organic bases. The crystal structure of the isomer of entacapone (Z-isomer), a significant human metabolite of E-isomer has been established. NMR methods for deriving E and Z geometry and other similar molecules have been successfully established, mainly by studying the proton coupled C-13 spectra. Preliminary studies reveal in vitro activity for some compounds against tuberculosis (TB) and dengue.

Fingerprinting environmental conditions and related stress using stable isotopic composition of rice (Oryza sativa L.) grain organic matter

Sea level rise (SLR) is a primary factor responsible for inundation of low-lying coastal regions across the world, which in turn governs the agricultural productivity. In this study, rice (Oryza sativa L.) cultivated seasonally in the Kuttanad Wetland, a SLR prone region on the southwest coast of India, were analysed for oxygen, hydrogen and carbon isotopic ratios (delta O-18, delta H-2 and delta C-13) to distinguish the seasonal environmental conditions prevalent during rice cultivation. The region receives high rainfall during the wet season which promotes large supply of fresh water to the local water bodies via the rivers. In contrast, during the dry season reduced river discharge favours sea water incursion which adversely affects the rice cultivation. The water for rice cultivation is derived from regional water bodies that are characterised by seasonal salinity variation which co-varies with the delta O-18 and delta H-2 values. Rice cultivated during the wet and the dry season bears the isotopic imprints of this water. We explored the utility of a mechanistic model to quantify the contribution of two prominent factors, namely relative humidity and source water composition in governing the seasonal variation in oxygen isotopic composition of rice grain OM. delta C-13 values of rice grain OM were used to deduce the stress level by estimating the intrinsic water use efficiency (WUEi) of the crop during the two seasons. 1.3 times higher WUE, was exhibited by the same genotype during the dry season. The approach can be extended to other low lying coastal agro-ecosystems to infer the growth conditions of cultivated crops and can further be utilised for retrieving paleo-environmental information from well preserved archaeological plant remains. (c) 2015 Elsevier Ltd. All rights reserved.

Structural characterization and in vitro biomedical activities of sulfated chitosan from Sepia pharaonis

A low molecular weight sulfated chitosan (SP-LMWSC) was isolated from the cuttlebone of Sepia pharaonis. Elemental analysis established the presence of C, H and N. The sulfation of SP-LMWSC was confirmed by the presence of characteristic peaks in FT-IR and FT-Raman spectra. The thermal properties of SP-LMWSC were studied by thermogravimetric analysis and differential scanning calorimetry. Electrolytic conductivity of SP-LMWSC was measured by cyclic voltammetry and the molecular weight was determined by MALDI-TOF/MS. The molecular structure and sulfation sites of SP-LMWSC were unambiguously confirmed using H-1,C-13, 2D COSY and 2D HSQC NMR spectroscopy. SP-LMWSC exhibited increased anticoagulant activity in avian blood by delaying coagulation parameters and displayed cytostatic activity by inhibiting the migration of avian leucocytes. SP-LMWSC demonstrated avian antiviral activity by binding to Newcastle disease virus receptors at a low titer value of 1/64. These findings suggested that SP-LMWSC isolated from an industrial discard holds immense potentials as carbohydrate based pharmaceuticals in future. (C) 2015 Elsevier B.V. All rights reserved.